DATA 550 Final Project Description

Allison Codi

This repository contains code to conduct analyses for the AntiBiotics for Children with Diarrhea (ABCD) clinical trial.

The repository has been broken into the following subfolders:

• data/ contains the simulated ABCD dataset and a data dictionary for the dataset

  • abcd_simulated_data550.csv is the dataset and will be loaded through the R scripts to conduct analyses
  • ABCD_OTR_Data Dictionary_SimulationData.xlsx is a data dictionary for the simulated dataset for user reference (not needed by any scripts in repository)

• R/ contains all necessary scripts to create the tables, figures, and models

  • 00_load_abcd_data.R is run first to load and format the data. It is sourced by the other R scripts.
  • 01_make_tables.R is run second to create relevant tables describing the dataset
  • 02_make_figures.R is run third to create figures for the single pathogen quantities
  • 03_fit_model.R is run fourth to fit the model and create a figure corresponding to the model

• output/ contains all relevant output produced from the R scripts to be knit into the final report (not pushed to GitHub, can be generated via running scripts)

• report.Rmd is the Markdown document that knits together the figures and tables into the final report

• render_report.R renders the final R Markdown report from the command line

• Makefile can be used to build the final report. It contains rules for making the tables, figures, and model. It also has a rule to clean up any undesired output. To build the final html report from scratch, run the make command